EPCS programing to custom board

after talking with altera people here is the conclusions:

if you are having problems with the flash programmer, I strongly recommend you upgrade to Quartus 5.1 and nios5.1. most of the problems with the flash programmer have been resolved in this release, and there is more debugging data available in the 5.1 release.

if you need to program the EPCS under 4.2, here are a few hints.

you need a tri state bridge in the mk_target_board design, even though you don't require it, a bug in the software makes it necessary.

ensure the target board design has a PLL and reset delay componet, just like the standard reference designs, and ensure the clock settings in the SOPC builder design are correct.